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Laboratory of Genetic Engineering, Institute of Biotechnology, Vietnam Academy of Science and Technology

Dang Hung Tran

Hanoi National University of Education

Cuong Nguyen

Vinmec Research Institute of Stem Cell and Gene Technology

Abstract

The development of next-generation sequencing technologies has helped sequence large genomes easily, producing a huge number of short-reads - small fragments of DNA. Despite the existence of many developed alignment tools, mapping short-read datasets to the reference genome, a crucial step of genome analysis, still remains a challenge. In this study, we develop a short-read alignment program, BWTaligner, based on the Burrows-Wheeler transform compression - exact and inexact matching. We tested it on the paired-end read data simulated from chromosome 9 of the rice genome to compare the alignment and single-nucleotide polymorphism (SNP) calling between our aligner and BWA - the preferred alignment program. The results showed that the BWA delivers higher recall and F-score, while BWTaligner has better precision in high coverage depth.

VJSTE is the official scientific outlet of the Ministry of Science and Technology, Vietnam, founded in 1959 and has been one of the prestigious scientific journals in Vietnam. VJSTE aims to become an international journal which meets the standards of the world leading databases of science journals such as Scopus, Web of Science, etc.